Teal Module: Forest Response Plot teal module

Usage

tm_g_forest_rsp(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  arm_ref_comp = NULL,
  paramcd,
  aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVALC"), "AVALC", fixed = TRUE),
  subgroup_var,
  strata_var,
  fixed_symbol_size = TRUE,
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  default_responses = c("CR", "PR", "Y", "Complete Response (CR)",
    "Partial Response (PR)"),
  plot_height = c(700L, 200L, 2000L),
  plot_width = c(900L, 200L, 2000L),
  pre_output = NULL,
  post_output = NULL,
  ggplot2_args = teal.widgets::ggplot2_args()
)

Arguments

label

(character)
menu item label of the module in the teal app.

dataname

(character)
analysis data used in teal module.

parentname

(character)
parent analysis data used in teal module, usually this refers to ADSL.

arm_var

(choices_selected or data_extract_spec)
object with all available choices and preselected option for variable names that can be used as arm_var. It defines the grouping variable(s) in the results table. If there are two elements selected for arm_var, second variable will be nested under the first variable.

arm_ref_comp

optional, (list)
If specified it must be a named list with each element corresponding to an arm variable in ADSL and the element must be another list (possibly with delayed teal.transform::variable_choices() or delayed teal.transform::value_choices() with the elements named ref and comp that the defined the default reference and comparison arms when the arm variable is changed.

paramcd

(choices_selected or data_extract_spec)
variable value designating the studied parameter.

aval_var

(choices_selected or data_extract_spec)
object with all available choices and preselected option for the analysis variable.

subgroup_var

(choices_selected or data_extract_spec)
object with all available choices and preselected option for variable names that can be used as the default subgroups.

strata_var

(choices_selected or data_extract_spec)
names of the variables for stratified analysis.

fixed_symbol_size

(logical)
When (TRUE), the same symbol size is used for plotting each estimate. Otherwise, the symbol size will be proportional to the sample size in each each subgroup.

conf_level

(choices_selected)
object with all available choices and preselected option for the confidence level, each within range of (0, 1).

default_responses

(list or character)
defines the default codes for the response variable in the module per value of paramcd. A passed vector is broadcasted for all paramcd values. A passed list must be named and contain arrays, each name corresponding to a single value of paramcd. Each array may contain default response values or named arrays rsp of default selected response values and levels of default level choices.

plot_height

optional, (numeric)
a vector of length three with c(value, min, max). Specifies the height of the main plot and renders a slider on the plot to interactively adjust the plot height.

plot_width

optional, (numeric)
a vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.

pre_output

optional, (shiny.tag)
with text placed before the output to put the output into context. For example a title.

post_output

optional, (shiny.tag)
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

ggplot2_args

optional, (ggplot2_args)
object created by teal.widgets::ggplot2_args() with settings for the module plot. For this module, this argument will only accept ggplot2_args object with labs list of following child elements: title, caption. No other elements would be taken into account. The argument is merged with option teal.ggplot2_args and with default module arguments (hard coded in the module body).

For more details, see the vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").

Author

Yuyao Song (songy24) yuyao.song@roche.com

Examples

library(scda)
library(dplyr)
library(nestcolor)

synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
ADSL <- synthetic_cdisc_data_latest$adsl
ADRS <- synthetic_cdisc_data_latest$adrs %>%
  mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
  filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")

arm_ref_comp <- list(
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  ),
  ARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL),
    cdisc_dataset("ADRS", ADRS),
    code =
      "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
       ADSL <- synthetic_cdisc_data_latest$adsl
       ADRS <- synthetic_cdisc_data_latest$adrs %>%
       mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
       filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')"
  ),
  modules = modules(
    tm_g_forest_rsp(
      label = "Forest Response",
      dataname = "ADRS",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADRS, "PARAMCD", "PARAM"),
        "INVET"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      ),
      plot_height = c(600L, 200L, 2000L),
      default_responses = list(
        BESRSPI = list(
          rsp = c("Stable Disease (SD)", "Not Evaluable (NE)"),
          levels = c(
            "Complete Response (CR)", "Partial Response (PR)", "Stable Disease (SD)",
            "Progressive Disease (PD)", "Not Evaluable (NE)"
          )
        ),
        INVET = list(
          rsp = c("Complete Response (CR)", "Partial Response (PR)"),
          levels = c(
            "Complete Response (CR)", "Not Evaluable (NE)", "Partial Response (PR)",
            "Progressive Disease (PD)", "Stable Disease (SD)"
          )
        ),
        OVRINV = list(
          rsp = c("Progressive Disease (PD)", "Stable Disease (SD)"),
          levels = c("Progressive Disease (PD)", "Stable Disease (SD)", "Not Evaluable (NE)")
        )
      )
    )
  )
)
#> [INFO] 2022-10-14 09:09:49.6409 pid:3139 token:[] teal.modules.clinical Initializing tm_g_forest_rsp
if (FALSE) {
shinyApp(app$ui, app$server)
}